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        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.26

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the bigbio/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2025-04-10, 12:10 UTC based on data in: /home/runner/work/pmultiqc/pmultiqc/data


        pmultiqc

        pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant.URL: https://github.com/bigbio/pmultiqc

        Experimental Design

        This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.

        You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 0/11 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        a05058
        1
        1
        1|2|3|4|5|6|7|8|9|10|11
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1|2|3|4|5|6|7|8|9|10|11
        a05059
        1
        2
        1|2|3|4|5|6|7|8|9|10|11
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1|2|3|4|5|6|7|8|9|10|11
        a05060
        1
        3
        1|2|3|4|5|6|7|8|9|10|11
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1|2|3|4|5|6|7|8|9|10|11
        a05061
        1
        4
        1|2|3|4|5|6|7|8|9|10|11
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1|2|3|4|5|6|7|8|9|10|11
        a05062
        1
        5
        1|2|3|4|5|6|7|8|9|10|11
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1|2|3|4|5|6|7|8|9|10|11
        a05063
        1
        6
        1|2|3|4|5|6|7|8|9|10|11
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1|2|3|4|5|6|7|8|9|10|11
        a05064
        1
        7
        1|2|3|4|5|6|7|8|9|10|11
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1|2|3|4|5|6|7|8|9|10|11
        a05065
        1
        8
        1|2|3|4|5|6|7|8|9|10|11
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1|2|3|4|5|6|7|8|9|10|11
        a05066
        1
        9
        1|2|3|4|5|6|7|8|9|10|11
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1|2|3|4|5|6|7|8|9|10|11
        a05067
        1
        10
        1|2|3|4|5|6|7|8|9|10|11
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1|2|3|4|5|6|7|8|9|10|11
        a05068
        1
        11
        1|2|3|4|5|6|7|8|9|10|11
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1|2|3|4|5|6|7|8|9|10|11

        MS1 Information

        MS1 quality control information extracted from the spectrum files

        TODO: add description here @Yasset

        Created with MultiQC

        MS1 base peak chromatograms extracted from the spectrum files

        TODO: add description here @Yasset

        Created with MultiQC

        MS1 Peaks from the spectrum files

        TODO: add description here @Yasset

        Created with MultiQC

        General stats for MS1 information from .d files

        TODO: add description here @Yasset

        Showing 0/11 rows and 3/3 columns.
        FileAcquisitionDateTimeTotalCurrentScanCurrent
        a05058
        2017-04-05 00:38:45
        20827918871396.2
        60618939978.0
        a05059
        2017-04-05 04:14:11
        15132807547826.2
        49337936803.1
        a05060
        2017-04-05 07:49:24
        24422877413510.5
        62980764225.7
        a05061
        2017-04-05 11:24:37
        27761323361699.8
        65305329464.2
        a05062
        2017-04-05 15:00:06
        24700757979462.0
        75678924854.1
        a05063
        2017-04-05 18:32:46
        24410995004332.0
        82900894832.7
        a05064
        2017-04-05 22:05:41
        27391217204231.0
        87654278664.7
        a05065
        2017-04-06 10:43:06
        21064319322662.5
        63257761242.4
        a05066
        2017-04-06 14:15:46
        25652785787778.5
        69488748440.2
        a05067
        2017-04-06 17:48:21
        25435332937856.0
        64289066969.3
        a05068
        2017-04-06 21:21:20
        5436747581850.0
        29151888716.8

        HeatMap

        This heatmap shows a performance overview of the pipeline

        This plot shows the pipeline performance overview. Some metrics are calculated.

        • Heatmap score[Contaminants]: as fraction of summed intensity with 0 = sample full of contaminants; 1 = no contaminants
        • Heatmap score[Pep Intensity (>23.0)]: Linear scale of the median intensity reaching the threshold, i.e. reaching 2^21 of 2^23 gives score 0.25.
        • Heatmap score[Charge]: Deviation of the charge 2 proportion from a representative Raw file (median). For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544 ).
        • Heatmap score [MC]: the fraction (0% - 100%) of fully cleaved peptides per Raw file
        • Heatmap score [MC Var]: each Raw file is scored for its deviation from the ‘average’ digestion state of the current study.
        • Heatmap score [ID rate over RT]: Judge column occupancy over retention time. Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of identifications over time indicate potential for LC gradient optimization.Scored using ‘Uniform’ scoring function. i.e. constant receives good score, extreme shapes are bad.
        • Heatmap score [MS2 Oversampling]: The percentage of non-oversampled 3D-peaks. An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file. For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides.
        • Heatmap score [Pep Missing]: Linear scale of the fraction of missing peptides.
        Created with MultiQC

        Summary Table

        This table shows the quantms pipeline summary statistics.

        This table shows the quantms pipeline summary statistics.

        Showing 0/1 rows and 5/5 columns.
        #MS2 Spectra#Identified MS2 Spectra%Identified MS2 Spectra#Peptides Identified#Proteins Identified#Proteins Quantified
        433836
        154772
        35.68%
        90555
        9655
        9655

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result.

        Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

        Showing 0/11 rows and 7/7 columns.
        Spectra FileSample NameConditionFraction#Peptide IDs#Unambiguous Peptide IDs#Modified Peptide IDs#Protein (group) IDs
        a05058
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1
        12495
        11321
        12495
        5631
        a05059
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        2
        13568
        12325
        13568
        6045
        a05060
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        3
        13003
        11783
        13003
        5875
        a05061
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        4
        13433
        12260
        13433
        5902
        a05062
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        5
        14216
        12956
        14216
        6159
        a05063
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        6
        18009
        16369
        18009
        6420
        a05064
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        7
        16285
        14718
        16285
        6068
        a05065
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        8
        14215
        13004
        14215
        6077
        a05066
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        9
        14554
        13271
        14554
        6093
        a05067
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        10
        13765
        12537
        13765
        6024
        a05068
        1|2|3|4|5|6|7|8|9|10|11
        SP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        11
        12
        12
        12
        10

        Number of Peptides identified Per Protein

        This plot shows the number of peptides per protein in quantms pipeline final result

        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

        Created with MultiQC

        Spectra Tracking

        This plot shows the tracking of the number of spectra along the quantms pipeline

        This table shows the changes in the number of spectra corresponding to each input file during the pipeline operation. And the number of peptides finally identified and quantified is obtained from the PSM table in the mzTab file. You can also remove decoys with the remove_decoy parameter.:

        • MS1_Num: The number of MS1 spectra extracted from mzMLs
        • MS2_Num: The number of MS2 spectra extracted from mzMLs
        • MSGF: The Number of spectra identified by MSGF search engine
        • Comet: The Number of spectra identified by Comet search engine
        • Sage: The Number of spectra identified by Sage search engine
        • PSMs from quant. peptides: extracted from PSM table in mzTab file
        • Peptides quantified: extracted from PSM table in mzTab file
        Showing 0/11 rows and 6/6 columns.
        Spectra File#MS1 Spectra#MS2 SpectraMSGFComet#PSMs from quant. peptides#Peptides quantified
        a05058
        6870
        37330
        24401
        24117
        13935
        11763
        a05059
        6471
        37536
        24920
        24702
        14683
        13183
        a05060
        7266
        38047
        24711
        24518
        14027
        12475
        a05061
        7649
        37733
        24986
        24790
        14661
        12995
        a05062
        5657
        41445
        26957
        26729
        15121
        13672
        a05063
        5982
        42856
        29469
        29222
        18909
        17336
        a05064
        7075
        40809
        27720
        27427
        17667
        15735
        a05065
        5947
        40698
        26495
        26127
        15303
        13323
        a05066
        6051
        41078
        26992
        26761
        15630
        13808
        a05067
        6062
        39997
        26228
        25738
        14819
        13170
        a05068
        4297
        36307
        17727
        17634
        17
        12

        Summary of Search Engine Scores

        These plots contain search scores and PEPs counts for different search engines in different files, and they also contain a summary of the consensus PSMs if two or more search engines are used.


        SpecEvalue Description

        This statistic is extracted from idXML files. SpecEvalue: Spectral E-values, the search score of MSGF. The value used for plotting is -lg(SpecEvalue).

        Created with MultiQC

        xcorr description

        This statistic is extracted from idXML files. xcorr: cross-correlation scores, the search score of Comet. The value used for plotting is xcorr.

        Created with MultiQC

        Summary of Posterior Error Probabilities (PEP)

        This statistic is extracted from idXML files.

        Created with MultiQC

        Summary of consensus support for PSMs

        Consensus support is a measure of agreement between search engines. Every peptide sequence in the analysis has been identified by at least one search run. The consensus support defines which fraction (between 0 and 1) of the remaining search runs "supported" a peptide identification that was kept. The meaning of "support" differs slightly between algorithms: For best, worst, average and rank, each search run supports peptides that it has also identified among its top considered_hits candidates. So the "consensus support" simply gives the fraction of additional search engines that have identified a peptide. (For example, if there are three search runs, peptides identified by two of them will have a "support" of 0.5.) For the similarity-based algorithms PEPMatrix and PEPIons, the "support" for a peptide is the average similarity of the most-similar peptide from each (other) search run.

        Created with MultiQC

        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

        Created with MultiQC

        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment.

        This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

        Created with MultiQC

        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

        Created with MultiQC

        Oversampling Distribution

        An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file.

        For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides. Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic exclusion windows for data independent acquisitions.

        • Heatmap score [EVD: MS2 Oversampling]: The percentage of non-oversampled 3D-peaks.
        Created with MultiQC

        Delta Mass

        This chart represents the distribution of the relative frequency of experimental precursor ion mass (m/z) - theoretical precursor ion mass (m/z).

        Mass deltas close to zero reflect more accurate identifications and also that the reporting of the amino acid modifications and charges have been done accurately. This plot can highlight systematic bias if not centered on zero. Other distributions can reflect modifications not being reported properly. Also it is easy to see the different between the target and the decoys identifications.

        Created with MultiQC

        Peptides Quantification Table

        This plot shows the quantification information of peptides in the final result (mainly the mzTab file).

        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.

        • BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets.
        • Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored.
        • Peptide intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately.
        Showing 0/50 rows and 7/7 columns.
        PeptideIDProtein NamePeptide SequenceBest Search ScoreAverage IntensitySP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1
        sp|P55011|S12A2_HUMAN
        AAAAAAAAAAAAAAAGAGAGAK
        0.9999
        5.1101
        5.0860
        5.1404
        5.0960
        2
        sp|Q99453|PHX2B_HUMAN
        AAAAAAAAAK
        1.0000
        5.9295
        5.9276
        5.9481
        5.9117
        3
        sp|Q96JP5|ZFP91_HUMAN
        AAAAAAAAAVSR
        1.0000
        4.2500
        4.2237
        4.2531
        4.2656
        4
        sp|Q5TF21|SOGA3_HUMAN
        AAAAAAAAQMHAK
        1.0000
        4.9208
        4.8813
        4.9496
        4.9193
        5
        sp|Q9Y4H2|IRS2_HUMAN
        AAAAAAAAVPSAGPAGPAPTSAAGR
        1.0000
        4.6795
        4.6525
        4.7113
        4.6659
        6
        sp|P36578|RL4_HUMAN
        AAAAAAALQAK
        1.0000
        5.6602
        5.6780
        5.6812
        5.6235
        7
        sp|O00178|GTPB1_HUMAN
        AAAAAAR
        0.9997
        4.1917
        4.0798
        4.2682
        4.1818
        8
        sp|Q6SPF0|SAMD1_HUMAN
        AAAAAATAPPSPGPAQPGPR
        0.9970
        4.5783
        4.5565
        4.5829
        4.5895
        9
        sp|O76031|CLPX_HUMAN
        AAAAADLANR
        1.0000
        4.9044
        4.8651
        4.9259
        4.9106
        10
        sp|Q8WUQ7|CATIN_HUMAN
        AAAAALSQQQSLQER
        1.0000
        3.5486
        3.4986
        3.5609
        3.5710
        11
        sp|A6NIH7|U119B_HUMAN
        AAAAASAAGPGGLVAGK
        1.0000
        4.5009
        4.4867
        4.5216
        4.4900
        12
        sp|Q9BTD8|RBM42_HUMAN
        AAAAATVVPPMVGGPPFVGPVGFGPGDR
        0.9997
        4.1653
        4.1245
        4.1983
        4.1603
        13
        sp|Q9P258|RCC2_HUMAN
        AAAAAWEEPSSGNGTAR
        1.0000
        4.8387
        4.8197
        4.8616
        4.8291
        14
        sp|Q99615|DNJC7_HUMAN
        AAAAECDVVMAATEPELLDDQEAK
        0.9989
        4.3740
        4.3483
        4.3851
        4.3813
        15
        sp|Q9Y2U8|MAN1_HUMAN
        AAAAGSLDR
        0.9999
        4.9444
        4.9107
        4.9686
        4.9437
        16
        sp|P0C0T4|RS25B_YEAST;sp|Q3E792|RS25A_YEAST
        AAAALAGGK
        0.9999
        5.8076
        6.0928
        5.7184
        5.4974
        17
        sp|Q15596|NCOA2_HUMAN
        AAAANIDEVQK
        1.0000
        4.1618
        4.1756
        4.1710
        4.1415
        18
        sp|Q9UPT8|ZC3H4_HUMAN
        AAAAPAATTATPPPEGAPPQPGVHNLPVPTLFGTVK
        1.0000
        4.4684
        4.4335
        4.5097
        4.4498
        19
        sp|Q96L91|EP400_HUMAN
        AAAAPFQTSQASASAPR
        0.9997
        4.2268
        4.1954
        4.2729
        4.2001
        20
        sp|P52701|MSH6_HUMAN
        AAAAPGASPSPGGDAAWSEAGPGPR
        1.0000
        5.3677
        5.4158
        5.3708
        5.3244
        21
        sp|P52701|MSH6_HUMAN
        AAAAPGASPSPGGDAAWSEAGPGPRPLAR
        1.0000
        3.5832
        3.5465
        3.6371
        3.5511
        22
        sp|P55036|PSMD4_HUMAN
        AAAASAAEAGIATTGTEDSDDALLK
        1.0000
        4.9622
        4.9446
        4.9947
        4.9408
        23
        sp|P09938|RIR2_YEAST
        AAADALSDLEIK
        0.9997
        4.8986
        5.1140
        4.8541
        4.6881
        24
        sp|O95159|ZFPL1_HUMAN
        AAADSDPNLDPLMNPHIR
        1.0000
        5.1045
        5.0664
        5.1372
        5.0980
        25
        sp|Q6P2E9|EDC4_HUMAN
        AAADTLQGPMQAAYR
        1.0000
        3.6096
        3.5992
        3.6228
        3.6039
        26
        sp|Q6P2E9|EDC4_HUMAN
        AAADTLQGPMQAAYR
        1.0000
        3.3063
        3.2023
        3.3229
        3.3557
        27
        sp|Q9NQP4|PFD4_HUMAN
        AAAEDVNVTFEDQQK
        1.0000
        4.0292
        3.9906
        4.0576
        4.0276
        28
        sp|O95551|TYDP2_HUMAN
        AAAEEGHIIPR
        1.0000
        5.4478
        5.3897
        5.4833
        5.4515
        29
        sp|O15357|SHIP2_HUMAN
        AAAEELLAR
        1.0000
        5.0724
        5.0563
        5.0820
        5.0745
        30
        sp|Q9H9Y2|RPF1_HUMAN
        AAAEELQEAAGAGDGATENGVQPPK
        1.0000
        4.5297
        4.4950
        4.5624
        4.5206
        31
        sp|Q96P70|IPO9_HUMAN
        AAAEEQIK
        0.9999
        5.2276
        5.1954
        5.2506
        5.2273
        32
        sp|P30260|CDC27_HUMAN
        AAAEGLMSLLR
        1.0000
        4.3024
        4.2771
        4.3361
        4.2854
        33
        sp|P00360|G3P1_YEAST
        AAAEGPMK
        0.9988
        3.9138
        4.1444
        3.8283
        3.7290
        34
        sp|P00360|G3P1_YEAST
        AAAEGPMK
        1.0000
        4.7633
        5.0495
        4.6743
        4.4495
        35
        sp|P15180|SYKC_YEAST
        AAAEGVANLHLDEATGEMVSK
        1.0000
        4.2037
        4.4023
        4.1753
        4.0020
        36
        sp|P15180|SYKC_YEAST
        AAAEGVANLHLDEATGEMVSK
        1.0000
        5.0252
        5.2850
        4.9685
        4.7316
        37
        sp|Q9NP50|SHCAF_HUMAN
        AAAEKPEEQGPEPLPISTQEW
        1.0000
        4.6442
        4.6190
        4.6637
        4.6425
        38
        sp|Q01780|EXOSX_HUMAN
        AAAEQAISVR
        1.0000
        4.9211
        4.9080
        4.9425
        4.9085
        39
        sp|O94766|B3GA3_HUMAN
        AAAEQLR
        0.9998
        4.8666
        4.8356
        4.8987
        4.8555
        40
        sp|Q02880|TOP2B_HUMAN
        AAAERPK
        0.9991
        5.2989
        5.2501
        5.3288
        5.3027
        41
        sp|P02786|TFR1_HUMAN
        AAAEVAGQFVIK
        0.9999
        5.7815
        5.7528
        5.8144
        5.7681
        42
        sp|P07954|FUMH_HUMAN
        AAAEVNQDYGLDPK
        1.0000
        5.1767
        5.1675
        5.1999
        5.1594
        43
        sp|P15705|STI1_YEAST
        AAAEYEK
        1.0000
        4.8083
        5.0531
        4.7440
        4.5642
        44
        sp|Q9Y490|TLN1_HUMAN
        AAAFEEQENETVVVK
        1.0000
        5.1944
        5.1751
        5.2089
        5.1939
        45
        sp|Q9P2E9|RRBP1_HUMAN
        AAAFEK
        0.9998
        5.5448
        5.5160
        5.5730
        5.5365
        46
        sp|O94826|TOM70_HUMAN
        AAAFEQLQK
        1.0000
        5.0643
        5.0542
        5.0947
        5.0397
        47
        sp|Q9H9Y2|RPF1_HUMAN
        AAAFPPGFSISEIK
        1.0000
        4.4674
        4.4606
        4.4868
        4.4522
        48
        sp|Q9Y6X3|SCC4_HUMAN
        AAAFYVR
        0.9997
        4.4727
        4.4467
        4.4918
        4.4721
        49
        sp|Q9P2E9|RRBP1_HUMAN
        AAAGEAK
        1.0000
        4.3334
        4.2981
        4.3611
        4.3302
        50
        sp|P23381|SYWC_HUMAN
        AAAGEDYK
        1.0000
        5.1423
        5.1080
        5.1395
        5.1689

        Protein Quantification Table

        This plot shows the quantification information of proteins in the final result (mainly the mzTab file).

        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.

        • Peptides_Number: The number of peptides for each protein.
        • Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored.
        • Protein intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of peptides.
        Showing 0/50 rows and 6/6 columns.
        ProteinIDProtein NameNumber of PeptidesAverage IntensitySP=Saccharomyces cerevisiae;CT=Mixture;QY=10%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=5%;CV=in-houseSP=Saccharomyces cerevisiae;CT=Mixture;QY=3.3%;CV=in-house
        1
        sp|A0A096LP55|QCR6L_HUMAN;sp|P07919|QCR6_HUMAN
        1
        3.7629
        3.7228
        3.7953
        3.7581
        2
        sp|A0A0B4J2D5|GAL3B_HUMAN;sp|P0DPI2|GAL3A_HUMAN
        9
        6.5573
        6.5406
        6.5786
        6.5475
        3
        sp|A0A0B4J2F0|PIOS1_HUMAN
        1
        4.2780
        4.2463
        4.3042
        4.2739
        4
        sp|A0AVF1|IFT56_HUMAN
        3
        4.4387
        4.4337
        4.4436
        4.4376
        5
        sp|A0AVT1|UBA6_HUMAN
        31
        6.7475
        6.7247
        6.7693
        6.7418
        6
        sp|A0FGR8|ESYT2_HUMAN
        15
        6.2588
        6.2497
        6.2776
        6.2462
        7
        sp|A0JNW5|UH1BL_HUMAN
        5
        5.2052
        5.1740
        5.2309
        5.2013
        8
        sp|A0MZ66|SHOT1_HUMAN
        27
        6.3095
        6.2787
        6.3350
        6.3057
        9
        sp|A0PJW6|TM223_HUMAN
        3
        5.4129
        5.3812
        5.4432
        5.4043
        10
        sp|A0PK00|T120B_HUMAN
        1
        4.7299
        4.7075
        4.7537
        4.7216
        11
        sp|A1A4S6|RHG10_HUMAN
        6
        5.5921
        5.5618
        5.6207
        5.5843
        12
        sp|A1IGU5|ARH37_HUMAN
        1
        4.5503
        4.5026
        4.5592
        4.5746
        13
        sp|A1L020|MEX3A_HUMAN
        9
        6.0197
        5.9861
        6.0425
        6.0206
        14
        sp|A1L0T0|HACL2_HUMAN
        14
        6.1952
        6.1741
        6.2165
        6.1891
        15
        sp|A1L157|TSN11_HUMAN
        1
        4.4176
        4.3933
        4.4480
        4.4036
        16
        sp|A1L170|CA226_HUMAN
        1
        4.3816
        4.3458
        4.3944
        4.3942
        17
        sp|A1L390|PKHG3_HUMAN
        5
        5.0416
        4.9997
        5.0701
        5.0423
        18
        sp|A1X283|SPD2B_HUMAN
        36
        6.7276
        6.7006
        6.7492
        6.7250
        19
        sp|A1XBS5|FA92A_HUMAN
        1
        3.8100
        3.7434
        3.8548
        3.8091
        20
        sp|A2AJT9|BCLA3_HUMAN
        3
        5.1031
        5.0738
        5.1206
        5.1064
        21
        sp|A2RRD8|ZN320_HUMAN
        1
        4.3234
        4.2796
        4.3412
        4.3363
        22
        sp|A2RRP1|NBAS_HUMAN
        30
        6.4328
        6.3973
        6.4582
        6.4323
        23
        sp|A2RTX5|SYTC2_HUMAN
        1
        4.1704
        4.1527
        4.1942
        4.1588
        24
        sp|A2RU67|F234B_HUMAN
        2
        4.7223
        4.7009
        4.7357
        4.7243
        25
        sp|A2RUC4|TYW5_HUMAN
        4
        5.0917
        5.0634
        5.1187
        5.0844
        26
        sp|A3KMH1|VWA8_HUMAN
        33
        6.4954
        6.5007
        6.5080
        6.4784
        27
        sp|A3KN83|SBNO1_HUMAN
        18
        6.1917
        6.1675
        6.2129
        6.1877
        28
        sp|A4D161|F221A_HUMAN
        5
        5.2597
        5.2262
        5.2892
        5.2533
        29
        sp|A4D1E9|GTPBA_HUMAN
        5
        5.6777
        5.6564
        5.6990
        5.6714
        30
        sp|A4D1P6|WDR91_HUMAN
        13
        5.9108
        5.8814
        5.9328
        5.9095
        31
        sp|A4D1U4|DEN11_HUMAN
        3
        4.5285
        4.4789
        4.5649
        4.5257
        32
        sp|A4D2B0|MBLC1_HUMAN
        2
        4.1057
        4.0507
        4.1030
        4.1454
        33
        sp|A5D8V6|VP37C_HUMAN
        3
        5.1016
        5.0754
        5.1207
        5.1012
        34
        sp|A5PLL7|PDES1_HUMAN
        2
        5.1872
        5.1639
        5.2028
        5.1883
        35
        sp|A5PLN9|TPC13_HUMAN
        3
        5.6313
        5.5989
        5.6598
        5.6251
        36
        sp|A5YKK6|CNOT1_HUMAN
        53
        6.9213
        6.8919
        6.9446
        6.9186
        37
        sp|A6H8Y1|BDP1_HUMAN
        2
        4.9599
        4.9276
        4.9915
        4.9504
        38
        sp|A6NC57|ANR62_HUMAN
        1
        3.3462
        3.2325
        3.3558
        3.4070
        39
        sp|A6NCE7|MP3B2_HUMAN;sp|Q9GZQ8|MLP3B_HUMAN
        2
        5.3332
        5.3261
        5.3676
        5.3015
        40
        sp|A6NCS6|CB072_HUMAN
        4
        4.7068
        4.6902
        4.7139
        4.7118
        41
        sp|A6ND36|FA83G_HUMAN
        3
        4.9101
        4.9036
        4.9309
        4.8935
        42
        sp|A6NDB9|PALM3_HUMAN
        11
        5.7112
        5.6822
        5.7320
        5.7110
        43
        sp|A6NDE4|RBY1B_HUMAN;sp|A6NEQ0|RBY1E_HUMAN;sp|P0C7P1|RBY1D_HUMAN;sp|P0DJD3|RBY1A_HUMAN;sp|P0DJD4|RBY1C_HUMAN;sp|Q15415|RBY1F_HUMAN
        1
        4.7747
        4.7245
        4.7941
        4.7901
        44
        sp|A6NDG6|PGP_HUMAN
        5
        5.8649
        5.8390
        5.8840
        5.8643
        45
        sp|A6NDU8|CE051_HUMAN
        2
        4.8114
        4.7871
        4.8268
        4.8133
        46
        sp|A6NDX5|ZN840_HUMAN
        1
        4.3298
        4.2876
        4.3691
        4.3187
        47
        sp|A6NED2|RCCD1_HUMAN
        3
        4.7508
        4.7096
        4.7662
        4.7645
        48
        sp|A6NFI3|ZN316_HUMAN
        2
        4.9098
        4.8857
        4.9296
        4.9071
        49
        sp|A6NGN9|IGLO5_HUMAN
        2
        5.0687
        5.0540
        5.0837
        5.0642
        50
        sp|A6NHL2|TBAL3_HUMAN
        1
        4.0439
        3.9831
        4.0709
        4.0582

        bigbio/quantms Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/bigbio/quantms

        Methods

        Data was processed using bigbio/quantms v1.4.0dev (doi: 10.5281/zenodo.7754148) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.10.5 (Di Tommaso et al., 2017) with the following command:

        nextflow run main.nf --input /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683/PXD007683-LFQ.sdrf.tsv --database /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683/uniprot-UP000005640_UP000002311_reviewed.fasta --add_decoys true --search_engines msgf,comet -resume PXD007683 -c /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/k8s_next.config -profile docker --ms2rescore true --ms2pip_model_dir /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/model_file/ --root_folder /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683 --local_input_type raw --ms2pip_model HCD --outdir ./PXD007683_msgf_comet_ms2rescore_quant --skip_post_msstats true

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        CONSENSUSIDConsensusID3.3.0-pre-exported-20250122
        DECOYDATABASEDecoyDatabase3.3.0-pre-exported-20250122
        FDRCONSENSUSIDFalseDiscoveryRate3.3.0-pre-exported-20250122
        IDFILTERIDFilter3.3.0-pre-exported-20250122
        MS2RESCOREMS2Rescore3.1.4
        deeplc3.1.8
        ms2pip4.1.0
        quantms-rescoring0.0.5
        MSGFDBINDEXINGmsgf_plusMS-GF+ Release (v2024.03.26) (26 March 2024)
        MZMLSTATISTICSquantms-utils0.0.20
        PERCOLATORPercolatorAdapter3.3.0-pre-exported-20250122
        percolator3.05.0, Build Date Aug 31 2020 19:03:04
        PROTEOMICSLFQProteomicsLFQ3.3.0-pre-exported-20250122
        SAMPLESHEET_CHECKquantms-utils0.0.20
        SDRFPARSINGsdrf-pipelines0.0.31
        SEARCHENGINECOMETComet2023.01 rev. 2
        CometAdapter3.3.0-pre-exported-20250122
        SEARCHENGINEMSGFMSGFPlusAdapter3.3.0-pre-exported-20250122
        msgf_plusMS-GF+ Release (v2023.01.12) (12 January 2023)
        THERMORAWFILEPARSERThermoRawFileParser1.3.4
        WorkflowNextflow24.10.5
        bigbio/quantmsv1.4.0dev

        bigbio/quantms Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/bigbio/quantms

        Input/output options

        export_decoy_psm
        true
        input
        /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683/PXD007683-LFQ.sdrf.tsv
        local_input_type
        raw
        outdir
        ./PXD007683_msgf_comet_ms2rescore_quant
        root_folder
        /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683

        SDRF validation

        skip_factor_validation
        true
        use_ols_cache_only
        true
        validate_ontologies
        true

        Protein database

        add_decoys
        true
        database
        /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/PXD007683/uniprot-UP000005640_UP000002311_reviewed.fasta

        Database search

        search_engines
        msgf,comet

        Modification localization

        luciphor_debug
        0

        PSM re-scoring (general)

        ms2pip_model
        HCD
        ms2pip_model_dir
        /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/model_file/
        ms2rescore
        true
        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        0

        Consensus ID

        consensusid_considered_top_hits
        0
        min_consensus_support
        0

        Isobaric analyzer

        quant_activation_method
        HCD

        Protein Quantification (LFQ)

        feature_with_id_min_score
        0.10

        Statistical post-processing

        contrasts
        pairwise
        skip_post_msstats
        true

        Quality control

        enable_pmultiqc
        true
        pmultiqc_idxml_skip
        true

        Generic options

        trace_report_suffix
        2025-03-30_11-14-03

        Core Nextflow options

        configFiles
        /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/gitrepo/new_quantms/quantms/nextflow.config, /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/k8s_next.config
        containerEngine
        docker
        launchDir
        /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/gitrepo/new_quantms/quantms
        profile
        docker
        projectDir
        /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/gitrepo/new_quantms/quantms
        runName
        mad_hodgkin
        userName
        daicx
        workDir
        /mnt/daicx/pvc-afbfaa68-aa52-416c-b273-64fb016fd745/mcp/gitrepo/new_quantms/quantms/work